From 84b2cd91f2eebb6355823b561b60a6f7fe2db6bc Mon Sep 17 00:00:00 2001
From: Martyn Gigg <martyn.gigg@stfc.ac.uk>
Date: Fri, 19 Jul 2019 10:53:14 +0100
Subject: [PATCH] Define wrapper for np.testing.assert_almost_equal for np <
1.9.0
Avoids a huge performance bottleneck when running the function
in a tight loop.
---
.../test/python/mantid/plots/CMakeLists.txt | 3 +-
.../test/python/mantid/plots/ScalesTest.py | 10 +-
.../plugins/algorithms/CalculateFluxTest.py | 4 +-
.../algorithms/FractionalIndexingTest.py | 1 +
.../DirectILLApplySelfShieldingTest.py | 14 +-
.../DirectILLCollectDataTest.py | 26 ++--
.../DirectILLReductionTest.py | 10 +-
.../DirectILLSelfShieldingTest.py | 7 +-
.../ReflectometryILLPreprocessTest.py | 22 ++--
.../test/testhelpers/__init__.py | 123 +++++++++++++++++-
.../ILLDetectorEfficiencyCorUserTest.py | 10 +-
.../plotting/test/test_figureinteraction.py | 2 +-
scripts/test/CrystalFieldMultiSiteTest.py | 12 +-
13 files changed, 184 insertions(+), 60 deletions(-)
diff --git a/Framework/PythonInterface/test/python/mantid/plots/CMakeLists.txt b/Framework/PythonInterface/test/python/mantid/plots/CMakeLists.txt
index 568495accf0..dfc7e590e48 100644
--- a/Framework/PythonInterface/test/python/mantid/plots/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/mantid/plots/CMakeLists.txt
@@ -6,7 +6,8 @@ set(TEST_PY_FILES
helperfunctionsTest.py
plotfunctionsTest.py
plotfunctions3DTest.py
- plots__init__Test.py)
+ plots__init__Test.py
+ ScalesTest.py)
check_tests_valid(${CMAKE_CURRENT_SOURCE_DIR} ${TEST_PY_FILES})
diff --git a/Framework/PythonInterface/test/python/mantid/plots/ScalesTest.py b/Framework/PythonInterface/test/python/mantid/plots/ScalesTest.py
index 1fa0c3e8046..471c0da281e 100644
--- a/Framework/PythonInterface/test/python/mantid/plots/ScalesTest.py
+++ b/Framework/PythonInterface/test/python/mantid/plots/ScalesTest.py
@@ -18,7 +18,7 @@ import unittest
from matplotlib.scale import scale_factory
from mantid.plots.scales import PowerScale, SquareScale
import numpy as np
-
+import testhelpers
class ScalesTest(unittest.TestCase):
@@ -31,7 +31,7 @@ class ScalesTest(unittest.TestCase):
scale = PowerScale(None, gamma=gamma)
x = np.linspace(0, 10, 1)
transform = scale.get_transform()
- np.testing.assert_almost_equal(np.power(x, gamma),
+ testhelpers.assert_almost_equal(np.power(x, gamma),
transform.transform_non_affine(x))
def test_power_inverse_transform(self):
@@ -39,7 +39,7 @@ class ScalesTest(unittest.TestCase):
scale = PowerScale(None, gamma=gamma)
x = np.linspace(0, 10, 1)
inv_transform = scale.get_transform().inverted()
- np.testing.assert_almost_equal(np.power(x, 1./gamma),
+ testhelpers.assert_almost_equal(np.power(x, 1./gamma),
inv_transform.transform_non_affine(x))
@@ -51,7 +51,7 @@ class ScalesTest(unittest.TestCase):
scale = SquareScale(None)
x = np.linspace(0, 10, 1)
transform = scale.get_transform()
- np.testing.assert_almost_equal(np.power(x, 2),
+ testhelpers.assert_almost_equal(np.power(x, 2),
transform.transform_non_affine(x))
@@ -59,7 +59,7 @@ class ScalesTest(unittest.TestCase):
scale = SquareScale(None)
x = np.linspace(0, 10, 1)
inv_transform = scale.get_transform().inverted()
- np.testing.assert_almost_equal(np.sqrt(x),
+ testhelpers.assert_almost_equal(np.sqrt(x),
inv_transform.transform_non_affine(x))
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CalculateFluxTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/CalculateFluxTest.py
index a87a03a9b93..ccee5b80476 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CalculateFluxTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CalculateFluxTest.py
@@ -9,7 +9,7 @@ from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import CalculateFlux, CreateSampleWorkspace, FindDetectorsInShape, mtd
import numpy as np
-
+import testhelpers
class CalculateFluxTest(unittest.TestCase):
@@ -37,7 +37,7 @@ class CalculateFluxTest(unittest.TestCase):
expectation.fill(self.pixels_in_shape * 0.3)
expectation[50] = self.pixels_in_shape * 10.3
reality = mtd["flux"].readY(0)
- np.testing.assert_almost_equal(reality, expectation, decimal=6)
+ testhelpers.assert_almost_equal(reality, expectation, decimal=6)
if __name__ == "__main__":
unittest.main()
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py
index 90cf09d575a..55f7089ad77 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/FractionalIndexingTest.py
@@ -7,6 +7,7 @@
import unittest
import numpy as np
import numpy.testing as npt
+import testhelpers
from mantid.geometry import UnitCell
from mantid.simpleapi import CreatePeaksWorkspace, CreateSimulationWorkspace
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py
index d38d6f8c947..b42cb9e3fdc 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLApplySelfShieldingTest.py
@@ -10,7 +10,7 @@ from __future__ import (absolute_import, division, print_function)
from mantid.api import (mtd)
from mantid.simpleapi import (CloneWorkspace)
import numpy.testing
-from testhelpers import illhelpers, run_algorithm
+from testhelpers import assert_almost_equal, illhelpers, run_algorithm
import unittest
@@ -44,7 +44,7 @@ class DirectILLApplySelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), ws.getNumberHistograms())
ys = outWS.extractY()
originalYs = ws.extractY()
- numpy.testing.assert_almost_equal(ys, (1.0 - ecFactor) * originalYs)
+ assert_almost_equal(ys, (1.0 - ecFactor) * originalYs)
def testEmptyContainerSubtractionWithScaling(self):
ws = self._cloneTestWorkspace()
@@ -67,7 +67,7 @@ class DirectILLApplySelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), ws.getNumberHistograms())
ys = outWS.extractY()
originalYs = ws.extractY()
- numpy.testing.assert_almost_equal(ys, (1.0 - ecScaling * ecFactor) * originalYs)
+ assert_almost_equal(ys, (1.0 - ecScaling * ecFactor) * originalYs)
def testSelfShieldingCorrections(self):
ws = self._cloneTestWorkspace()
@@ -91,10 +91,10 @@ class DirectILLApplySelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), ws.getNumberHistograms())
ys = outWS.extractY()
originalYs = ws.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs / corrFactor)
+ assert_almost_equal(ys, originalYs / corrFactor)
es = outWS.extractE()
originalEs = ws.extractE()
- numpy.testing.assert_almost_equal(es, originalEs / corrFactor)
+ assert_almost_equal(es, originalEs / corrFactor)
def testNoOperationClonesInputWorkspace(self):
ws = self._cloneTestWorkspace()
@@ -127,10 +127,10 @@ class DirectILLApplySelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), ws.getNumberHistograms())
ys = outWS.extractY()
originalYs = ws.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs / corrFactor)
+ assert_almost_equal(ys, originalYs / corrFactor)
es = outWS.extractE()
originalEs = ws.extractE()
- numpy.testing.assert_almost_equal(es, originalEs / corrFactor)
+ assert_almost_equal(es, originalEs / corrFactor)
def _cloneTestWorkspace(self, wsName=None):
if not wsName:
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py
index 83d1f980f15..f040fd22723 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLCollectDataTest.py
@@ -8,7 +8,7 @@ from __future__ import (absolute_import, division, print_function)
from mantid.api import mtd
import numpy.testing
-from testhelpers import illhelpers, run_algorithm
+from testhelpers import assert_almost_equal, illhelpers, run_algorithm
import unittest
@@ -51,7 +51,7 @@ class DirectILLCollectDataTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), inWS.getNumberHistograms() - 1)
ys = outWS.extractY()
originalYs = inWS.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs[:-1, :] - self._BKG_LEVEL)
+ assert_almost_equal(ys, originalYs[:-1, :] - self._BKG_LEVEL)
def testBackgroundOutput(self):
outWSName = 'outWS'
@@ -70,7 +70,7 @@ class DirectILLCollectDataTest(unittest.TestCase):
run_algorithm('DirectILLCollectData', **algProperties)
self.assertTrue(mtd.doesExist(outBkgWSName))
outBkgWS = mtd[outBkgWSName]
- numpy.testing.assert_almost_equal(outBkgWS.extractY(), self._BKG_LEVEL)
+ assert_almost_equal(outBkgWS.extractY(), self._BKG_LEVEL)
def testNormalisationToTime(self):
outWSName = 'outWS'
@@ -90,10 +90,10 @@ class DirectILLCollectDataTest(unittest.TestCase):
inWS = mtd[self._TEST_WS_NAME]
ys = outWS.extractY()
originalYs = inWS.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs[:-1, :] / duration)
+ assert_almost_equal(ys, originalYs[:-1, :] / duration)
es = outWS.extractE()
originalEs = inWS.extractE()
- numpy.testing.assert_almost_equal(es, originalEs[:-1, :] / duration)
+ assert_almost_equal(es, originalEs[:-1, :] / duration)
def testNormalisationToTimeWhenMonitorCountsAreTooLow(self):
outWSName = 'outWS'
@@ -116,10 +116,10 @@ class DirectILLCollectDataTest(unittest.TestCase):
inWS = mtd[self._TEST_WS_NAME]
ys = outWS.extractY()
originalYs = inWS.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs[:-1, :] / duration)
+ assert_almost_equal(ys, originalYs[:-1, :] / duration)
es = outWS.extractE()
originalEs = inWS.extractE()
- numpy.testing.assert_almost_equal(es, originalEs[:-1, :] / duration)
+ assert_almost_equal(es, originalEs[:-1, :] / duration)
def testRawWorkspaceOutput(self):
outWSName = 'outWS'
@@ -138,13 +138,13 @@ class DirectILLCollectDataTest(unittest.TestCase):
rawWS = mtd[rawWSName]
ys = rawWS.extractY()
originalYS = inWS.extractY()
- numpy.testing.assert_almost_equal(ys, originalYS[:-1, :])
+ assert_almost_equal(ys, originalYS[:-1, :])
es = rawWS.extractE()
originalES = inWS.extractE()
- numpy.testing.assert_almost_equal(es, originalES[:-1, :])
+ assert_almost_equal(es, originalES[:-1, :])
xs = rawWS.extractX()
outXS = outWS.extractX()
- numpy.testing.assert_almost_equal(xs, outXS)
+ assert_almost_equal(xs, outXS)
Ei = rawWS.getRun().getProperty('Ei').value
outEi = outWS.getRun().getProperty('Ei').value
self.assertEqual(Ei, outEi)
@@ -170,13 +170,13 @@ class DirectILLCollectDataTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), inWS.getNumberHistograms() - 1)
xs = outWS.extractX()
originalXs = inWS.extractX()
- numpy.testing.assert_almost_equal(xs, originalXs[:-1, :])
+ assert_almost_equal(xs, originalXs[:-1, :])
ys = outWS.extractY()
originalYs = inWS.extractY()
- numpy.testing.assert_almost_equal(ys, originalYs[:-1, :])
+ assert_almost_equal(ys, originalYs[:-1, :])
es = outWS.extractE()
originalEs = inWS.extractE()
- numpy.testing.assert_almost_equal(es, originalEs[:-1, :])
+ assert_almost_equal(es, originalEs[:-1, :])
def testOutputIncidentEnergyWorkspaceWhenEnergyCalibrationIsOff(self):
outWSName = 'outWS'
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
index 495ec867bc0..f2c4b6d1ad2 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLReductionTest.py
@@ -10,7 +10,7 @@ import collections
from mantid.api import mtd
import numpy
import numpy.testing
-from testhelpers import illhelpers, run_algorithm
+from testhelpers import assert_almost_equal, illhelpers, run_algorithm
import unittest
@@ -154,7 +154,7 @@ class DirectILLReductionTest(unittest.TestCase):
ws = mtd[outWSName]
self.assertEqual(ws.getAxis(0).getUnit().unitID(), 'DeltaE')
xs = ws.readX(0)
- numpy.testing.assert_almost_equal(xs, numpy.arange(E0, E1 + 0.01, dE))
+ assert_almost_equal(xs, numpy.arange(E0, E1 + 0.01, dE))
def testHybridERebinningSingleUserRange(self):
outWSName = 'outWS'
@@ -173,7 +173,7 @@ class DirectILLReductionTest(unittest.TestCase):
ws = mtd[outWSName]
self.assertEqual(ws.getAxis(0).getUnit().unitID(), 'DeltaE')
xs = ws.readX(0)
- numpy.testing.assert_almost_equal(xs, numpy.arange(E0, E1 + 0.01, dE))
+ assert_almost_equal(xs, numpy.arange(E0, E1 + 0.01, dE))
def testHybridERebinningUserConstrainedAutoRange(self):
outWSName = 'outWS'
@@ -211,7 +211,7 @@ class DirectILLReductionTest(unittest.TestCase):
ws = mtd[outWSName]
self.assertEqual(ws.getAxis(0).getUnit().unitID(), 'MomentumTransfer')
xs = ws.readX(0)
- numpy.testing.assert_almost_equal(xs, numpy.arange(Q0, Q1, dQ))
+ assert_almost_equal(xs, numpy.arange(Q0, Q1, dQ))
def testQRebinningBinWidthOnly(self):
_add_natural_angle_step_parameter(self._TEST_WS_NAME)
@@ -231,7 +231,7 @@ class DirectILLReductionTest(unittest.TestCase):
self.assertGreater(len(xs), 3)
dx = xs[1:] - xs[:-1]
# Bin widths may differ at the edges.
- numpy.testing.assert_almost_equal(dx[1:-1], 0.1)
+ assert_almost_equal(dx[1:-1], 0.1)
def _checkAlgorithmsInHistory(self, ws, *args):
"""Return true if algorithm names listed in *args are found in the
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py
index 3a0bd040d86..94f2f7bae40 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/DirectILLSelfShieldingTest.py
@@ -6,9 +6,8 @@
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)
-from testhelpers import illhelpers, run_algorithm
+from testhelpers import assert_almost_equal, illhelpers, run_algorithm
from mantid.api import mtd
-import numpy.testing
import unittest
@@ -58,7 +57,7 @@ class DirectILLSelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), inWS.getNumberHistograms())
xs = outWS.extractX()
originalXs = inWS.extractX()
- numpy.testing.assert_almost_equal(xs, originalXs[:, :])
+ assert_almost_equal(xs, originalXs[:, :])
def testOutputHasCommonBinningWithInput(self):
self._setDefaultSample(self._TEST_WS_NAME)
@@ -75,7 +74,7 @@ class DirectILLSelfShieldingTest(unittest.TestCase):
self.assertEqual(outWS.getNumberHistograms(), inWS.getNumberHistograms())
xs = outWS.extractX()
originalXs = inWS.extractX()
- numpy.testing.assert_almost_equal(xs, originalXs[:, :])
+ assert_almost_equal(xs, originalXs[:, :])
def _setDefaultSample(self, wsName):
geometry = {
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/ReflectometryILLPreprocessTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/ReflectometryILLPreprocessTest.py
index f6f0bbe9209..57fcf4ae427 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/ReflectometryILLPreprocessTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/WorkflowAlgorithms/ReflectometryILLPreprocessTest.py
@@ -11,7 +11,7 @@ from __future__ import (absolute_import, division, print_function)
from mantid.api import mtd
from mantid.simpleapi import ReflectometryILLPreprocess
import numpy.testing
-from testhelpers import (assertRaisesNothing, create_algorithm, illhelpers)
+from testhelpers import (assertRaisesNothing, assert_almost_equal, create_algorithm, illhelpers)
import unittest
import ReflectometryILL_common as common
@@ -84,9 +84,9 @@ class ReflectometryILLPreprocessTest(unittest.TestCase):
for i in range(outWS.getNumberHistograms()):
ys = outWS.readY(i)
if i != 49:
- numpy.testing.assert_almost_equal(ys, [0.0] * ysSize, decimal=12)
+ assert_almost_equal(ys, [0.0] * ysSize, decimal=12)
else:
- numpy.testing.assert_almost_equal(ys, [10.0] * ysSize, decimal=12)
+ assert_almost_equal(ys, [10.0] * ysSize, decimal=12)
self.assertEqual(mtd.getObjectNames(), ['ReflectometryILLPreprocess_test_ws'])
def _backgroundSubtraction(self, subtractionType):
@@ -113,9 +113,9 @@ class ReflectometryILLPreprocessTest(unittest.TestCase):
for i in range(outWS.getNumberHistograms()):
ys = outWS.readY(i)
if i != 49:
- numpy.testing.assert_almost_equal(ys, [0.0] * ysSize)
+ assert_almost_equal(ys, [0.0] * ysSize)
else:
- numpy.testing.assert_almost_equal(ys, [10.0] * ysSize)
+ assert_almost_equal(ys, [10.0] * ysSize)
self.assertEqual(mtd.getObjectNames(), ['ReflectometryILLPreprocess_test_ws'])
def testLinearFlatBackgroundSubtraction(self):
@@ -199,17 +199,17 @@ class ReflectometryILLPreprocessTest(unittest.TestCase):
for i in range(outWS.getNumberHistograms()):
ys = outWS.readY(i)
if i in lowerBkgIndices:
- numpy.testing.assert_almost_equal(ys, [0.0] * ysSize)
+ assert_almost_equal(ys, [0.0] * ysSize)
elif i in lowerExclusionIndices:
- numpy.testing.assert_almost_equal(ys, [-1005.0] * ysSize)
+ assert_almost_equal(ys, [-1005.0] * ysSize)
elif i in foregroundIndices:
- numpy.testing.assert_almost_equal(ys, [995.0] * ysSize)
+ assert_almost_equal(ys, [995.0] * ysSize)
elif i in upperExclusionIndices:
- numpy.testing.assert_almost_equal(ys, [-1005.0] * ysSize)
+ assert_almost_equal(ys, [-1005.0] * ysSize)
elif i in upperBkgIndices:
- numpy.testing.assert_almost_equal(ys, [0.0] * ysSize)
+ assert_almost_equal(ys, [0.0] * ysSize)
else:
- numpy.testing.assert_almost_equal(ys, [-5.0] * ysSize)
+ assert_almost_equal(ys, [-5.0] * ysSize)
self.assertEqual(mtd.getObjectNames(), ['ReflectometryILLPreprocess_test_ws'])
def testAsymmetricForegroundRanges(self):
diff --git a/Framework/PythonInterface/test/testhelpers/__init__.py b/Framework/PythonInterface/test/testhelpers/__init__.py
index ac62d537261..fae1de93f4e 100644
--- a/Framework/PythonInterface/test/testhelpers/__init__.py
+++ b/Framework/PythonInterface/test/testhelpers/__init__.py
@@ -10,13 +10,16 @@ are for use in unit tests only!
from __future__ import (absolute_import, division,
print_function)
+from distutils.version import LooseVersion
+
# Import mantid to set MANTIDPATH for any ConfigService call that may be done
import mantid # noqa
# Add workspace creation namespace
import WorkspaceCreationHelper
-# Define some pure-Python functions to add to the mix
+import numpy
+# Define some pure-Python functions to add to the mix
def run_algorithm(name, **kwargs):
"""Run a named algorithm and return the
@@ -101,3 +104,121 @@ def can_be_instantiated(cls):
except RuntimeError:
result = False
return result
+
+
+# Work around for slow testhelpers.assert_almost_equal that was fixed in 1.9.0:
+# - https://github.com/numpy/numpy/commit/79d3a94f41b7e3c661eceed2f26ba6cce362ba4f
+# Running assert_almost_equal in a tight loop with v<1.9.0 causes major slows (read minutes)
+if LooseVersion(numpy.__version__) >= LooseVersion("1.9.0"):
+ assert_almost_equal = numpy.testing.assert_almost_equal
+else:
+ def assert_almost_equal(actual,desired,decimal=7,err_msg='',verbose=True):
+ """
+ Raises an AssertionError if two items are not equal up to desired
+ precision.
+ .. note:: It is recommended to use one of `assert_allclose`,
+ `assert_array_almost_equal_nulp` or `assert_array_max_ulp`
+ instead of this function for more consistent floating point
+ comparisons.
+ The test is equivalent to ``abs(desired-actual) < 0.5 * 10**(-decimal)``.
+ Given two objects (numbers or ndarrays), check that all elements of these
+ objects are almost equal. An exception is raised at conflicting values.
+ For ndarrays this delegates to assert_array_almost_equal
+ Parameters
+ ----------
+ actual : array_like
+ The object to check.
+ desired : array_like
+ The expected object.
+ decimal : int, optional
+ Desired precision, default is 7.
+ err_msg : str, optional
+ The error message to be printed in case of failure.
+ verbose : bool, optional
+ If True, the conflicting values are appended to the error message.
+ Raises
+ ------
+ AssertionError
+ If actual and desired are not equal up to specified precision.
+ See Also
+ --------
+ assert_allclose: Compare two array_like objects for equality with desired
+ relative and/or absolute precision.
+ assert_array_almost_equal_nulp, assert_array_max_ulp, assert_equal
+ Examples
+ --------
+ >>> import numpy.testing as npt
+ >>> npt.assert_almost_equal(2.3333333333333, 2.33333334)
+ >>> npt.assert_almost_equal(2.3333333333333, 2.33333334, decimal=10)
+ ...
+ <type 'exceptions.AssertionError'>:
+ Items are not equal:
+ ACTUAL: 2.3333333333333002
+ DESIRED: 2.3333333399999998
+ >>> npt.assert_almost_equal(np.array([1.0,2.3333333333333]),
+ ... np.array([1.0,2.33333334]), decimal=9)
+ ...
+ <type 'exceptions.AssertionError'>:
+ Arrays are not almost equal
+ <BLANKLINE>
+ (mismatch 50.0%)
+ x: array([ 1. , 2.33333333])
+ y: array([ 1. , 2.33333334])
+ """
+ __tracebackhide__ = True # Hide traceback for py.test
+ from numpy.core import ndarray
+ from numpy.lib import iscomplexobj, real, imag
+ from numpy.testing.utils import (assert_array_almost_equal, build_err_msg,
+ gisfinite, gisnan)
+
+ # Handle complex numbers: separate into real/imag to handle
+ # nan/inf/negative zero correctly
+ # XXX: catch ValueError for subclasses of ndarray where iscomplex fail
+ try:
+ usecomplex = iscomplexobj(actual) or iscomplexobj(desired)
+ except ValueError:
+ usecomplex = False
+
+ def _build_err_msg():
+ header = ('Arrays are not almost equal to %d decimals' % decimal)
+ return build_err_msg([actual, desired], err_msg, verbose=verbose,
+ header=header)
+
+ if usecomplex:
+ if iscomplexobj(actual):
+ actualr = real(actual)
+ actuali = imag(actual)
+ else:
+ actualr = actual
+ actuali = 0
+ if iscomplexobj(desired):
+ desiredr = real(desired)
+ desiredi = imag(desired)
+ else:
+ desiredr = desired
+ desiredi = 0
+ try:
+ assert_almost_equal(actualr, desiredr, decimal=decimal)
+ assert_almost_equal(actuali, desiredi, decimal=decimal)
+ except AssertionError:
+ raise AssertionError(_build_err_msg())
+
+ if isinstance(actual, (ndarray, tuple, list)) \
+ or isinstance(desired, (ndarray, tuple, list)):
+ return assert_array_almost_equal(actual, desired, decimal, err_msg)
+ try:
+ # If one of desired/actual is not finite, handle it specially here:
+ # check that both are nan if any is a nan, and test for equality
+ # otherwise
+ if not (gisfinite(desired) and gisfinite(actual)):
+ if gisnan(desired) or gisnan(actual):
+ if not (gisnan(desired) and gisnan(actual)):
+ raise AssertionError(_build_err_msg())
+ else:
+ if not desired == actual:
+ raise AssertionError(_build_err_msg())
+ return
+ except (NotImplementedError, TypeError):
+ pass
+ if round(abs(desired - actual), decimal) != 0:
+ raise AssertionError(_build_err_msg())
diff --git a/Testing/SystemTests/tests/analysis/ILLDetectorEfficiencyCorUserTest.py b/Testing/SystemTests/tests/analysis/ILLDetectorEfficiencyCorUserTest.py
index ac712e242d1..255d5dfec62 100644
--- a/Testing/SystemTests/tests/analysis/ILLDetectorEfficiencyCorUserTest.py
+++ b/Testing/SystemTests/tests/analysis/ILLDetectorEfficiencyCorUserTest.py
@@ -7,9 +7,9 @@
from __future__ import (absolute_import, division, print_function)
import numpy
-import numpy.testing
import systemtesting
from mantid.simpleapi import (ConvertUnits, DetectorEfficiencyCorUser, DirectILLCollectData)
+from testhelpers import assert_almost_equal
class IN4(systemtesting.MantidSystemTest):
@@ -35,12 +35,12 @@ class IN4(systemtesting.MantidSystemTest):
for i in range(0, 300):
x = (corr.readX(i)[:-1] + corr.readX(i)[1:]) / 2.
e = Ei - x
- numpy.testing.assert_almost_equal(corr.readY(i), eff_factor(e, wide_angle_corr))
+ assert_almost_equal(corr.readY(i), eff_factor(e, wide_angle_corr))
# Rosace detectors are at ws indices 300-395
for i in range(300, 396):
x = (corr.readX(i)[:-1] + corr.readX(i)[1:]) / 2.
e = Ei - x
- numpy.testing.assert_almost_equal(corr.readY(i), eff_factor(e, rosace_corr))
+ assert_almost_equal(corr.readY(i), eff_factor(e, rosace_corr))
class IN5(systemtesting.MantidSystemTest):
@@ -60,7 +60,7 @@ class IN5(systemtesting.MantidSystemTest):
for i in range(corr.getNumberHistograms()):
x = (corr.readX(i)[:-1] + corr.readX(i)[1:]) / 2.
e = Ei - x
- numpy.testing.assert_almost_equal(corr.readY(i), corr_at_Ei / tube_corr(e))
+ assert_almost_equal(corr.readY(i), corr_at_Ei / tube_corr(e))
class IN6(systemtesting.MantidSystemTest):
@@ -85,4 +85,4 @@ class IN6(systemtesting.MantidSystemTest):
for i in range(corr.getNumberHistograms()):
x = (corr.readX(i)[:-1] + corr.readX(i)[1:]) / 2.
e = Ei - x
- numpy.testing.assert_almost_equal(corr.readY(i), corr_at_Ei / det_corr(e))
+ assert_almost_equal(corr.readY(i), corr_at_Ei / det_corr(e))
diff --git a/qt/applications/workbench/workbench/plotting/test/test_figureinteraction.py b/qt/applications/workbench/workbench/plotting/test/test_figureinteraction.py
index e01fc3f768c..137693774c7 100644
--- a/qt/applications/workbench/workbench/plotting/test/test_figureinteraction.py
+++ b/qt/applications/workbench/workbench/plotting/test/test_figureinteraction.py
@@ -16,8 +16,8 @@ import unittest
import matplotlib
matplotlib.use('AGG') # noqa
import numpy as np
-from numpy.testing import assert_almost_equal
from qtpy.QtCore import Qt
+from testhelpers import assert_almost_equal
# local package imports
from mantid.plots import MantidAxes
diff --git a/scripts/test/CrystalFieldMultiSiteTest.py b/scripts/test/CrystalFieldMultiSiteTest.py
index f9138fcf5a7..64d4d6d32f1 100644
--- a/scripts/test/CrystalFieldMultiSiteTest.py
+++ b/scripts/test/CrystalFieldMultiSiteTest.py
@@ -7,8 +7,10 @@
import numpy as np
import unittest
+import testhelpers
from CrystalField.CrystalFieldMultiSite import CrystalFieldMultiSite
+
c_mbsr = 79.5774715459 # Conversion from barn to mb/sr
@@ -121,7 +123,7 @@ class CrystalFieldMultiSiteTests(unittest.TestCase):
y = y / c_mbsr
expected_y = [12.474955, 1.190169, 0.122781, 0.042940, 10.837438]
np.testing.assert_equal(x, r)
- np.testing.assert_almost_equal(y, expected_y, 6)
+ testhelpers.assert_almost_equal(y, expected_y, 6)
def test_get_spectrum_ws(self):
from mantid.simpleapi import CreateWorkspace
@@ -159,13 +161,13 @@ class CrystalFieldMultiSiteTests(unittest.TestCase):
y = y / c_mbsr
expected_y = [12.474946, 1.190160, 0.122785, 0.042940, 10.837170]
np.testing.assert_equal(x, r)
- np.testing.assert_almost_equal(y, expected_y, 6)
+ testhelpers.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [6.304662, 0.331218, 1.224681, 0.078540, 2.638049]
np.testing.assert_equal(x, r)
- np.testing.assert_almost_equal(y, expected_y, 6)
+ testhelpers.assert_almost_equal(y, expected_y, 6)
def test_get_spectrum_ws_multi_spectra(self):
from mantid.simpleapi import CreateWorkspace
@@ -213,13 +215,13 @@ class CrystalFieldMultiSiteTests(unittest.TestCase):
y = y / c_mbsr
expected_y = [3.904037, 0.744519, 0.274897, 0.175713, 0.106540]
np.testing.assert_equal(x, r)
- np.testing.assert_almost_equal(y, expected_y, 6)
+ testhelpers.assert_almost_equal(y, expected_y, 6)
x, y = cfms.getSpectrum(1, r)
y = y / c_mbsr
expected_y = [3.704726, 0.785600, 0.296255, 0.190176, 0.115650]
np.testing.assert_equal(x, r)
- np.testing.assert_almost_equal(y, expected_y, 6)
+ testhelpers.assert_almost_equal(y, expected_y, 6)
def test_fit_multi_ion_single_spectrum(self):
--
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